1BP_UNFLATTEN_SEQ(1) User Contributed Perl Documentation BP_UNFLATTEN_SEQ(1)
2
6 unflatten_seq - unflatten a genbank or genbank-style feature file into
7 a nested SeqFeature hierarchy
8
10 unflatten_seq.PLS -e 3 -gff ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb
11 unflatten_seq.PLS --detail ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb
13 unflatten_seq.PLS -i foo.embl --from embl --to chadoxml -o out.chado.xml
15 unflatten_seq.PLS --notypemap --detail --to asciitree -ethresh 2 AE003644_Adh-genomic.gb
17
19 This script will unflatten a genbank or genbank-style file of
20 SeqFeatures into a nested hierarchy.
21 See Bio::SeqFeature::Tools::Unflattener
23 In a GenBank/EMBL representation, features are 'flat' - for example,
25 there is no link between an mRNA and a CDS, other than implicit links
26 (eg via tags or via splice site coordinates) which may be hard to code
27 for.
28 This is most easily illustrated with the default output format,
30 asciitree
31 An unflattened genbank feature set may look like this (AB077698)
33 Seq: AB077698
35 databank_entry 1..2701[+]
36 gene
37 mRNA
38 CDS hCHCR-G 80..1144[+]
39 exon 80..1144[+]
40 five_prime_UTR 1..79[+]
41 located_sequence_feature 137..196[+]
42 located_sequence_feature 239..292[+]
43 located_sequence_feature 617..676[+]
44 located_sequence_feature 725..778[+]
45 three_prime_UTR 1145..2659[+]
46 polyA_site 1606..1606[+]
47 polyA_site 2660..2660[+]
48 Or like this (portion of AE003734)
50 gene
52 mRNA CG3320-RA
53 CDS CG3320-PA 53126..54971[-]
54 exon 52204..53323[-]
55 exon 53404..53631[-]
56 exon 53688..53735[-]
57 exon 53798..53918[-]
58 exon 54949..55287[-]
59 mRNA CG3320-RB
60 CDS CG3320-PB 53383..54971[-]
61 exon 52204..53631[-]
62 exon 53688..53735[-]
63 exon 53798..53918[-]
64 exon 54949..55287[-]
65 The unflattening will also 'normalize' the containment hierarchy (in
67 the sense of standardising it - e.g. making sure there is always a
68 transcript record, even if genbank just specifies CDS and gene)
69 By default, the GenBank types will be mapped to SO types
71 See Bio::SeqFeature::Tools::TypeMapper
73
75 -i|input FILE
76 input file (can also be specified as last argument)
77 -from FORMAT
79 input format (defaults to genbank)
80 probably doesnt make so much sense to use this for non-flat
82 formats; ie other than embl/genbank
83 -to FORMAT
85 output format (defaults to asciitree)
86 should really be a format that is nested SeqFeature aware; I think
88 this is only asciitree, chadoxml and gff3
89 -gff
91 with export to GFF3 format (pre-3 GFFs make no sense with
92 unflattened sequences, as they have no set way of representing
93 feature graphs)
94 -o|output FILE
96 outfile defaults to STDOUT
97 -detail
99 show extra detail on features (asciitree mode only)
100 -e|ethresh INT
102 sets the error threshold on unflattening
103 by default this script will throw a wobbly if it encounters weird
105 stuff in the genbank file - raise the error threshold to signal
106 these to be ignored (and reported on STDERR)
107 -nomagic
109 suppress use_magic in unflattening (see
110 Bio::SeqFeature::Tools::Unflattener
111 -notypemap
113 suppress type mapping (see Bio::SeqFeature::Tools::TypeMapper
114
116 Bio::SeqFeature::Tools::Unflattener allows fine-grained control over
117 the unflattening process - need to add more options to allow this
118 control at the command line
119
121 Mailing Lists
122 User feedback is an integral part of the evolution of this and other
123 Bioperl modules. Send your comments and suggestions preferably to the
124 Bioperl mailing list. Your participation is much appreciated.
125 bioperl-l@bioperl.org - General discussion
127 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
128 Reporting Bugs
130 Report bugs to the Bioperl bug tracking system to help us keep track of
131 the bugs and their resolution. Bug reports can be submitted via email
132 or the web:
133 http://bugzilla.open-bio.org/
135
137 Chris Mungall E<lt>cjm-at-bioperl.orgE<gt>
138perl v5.12.0 2010-04-29 BP_UNFLATTEN_SEQ(1)